Simple identification tools in FishBase

Simple identification tools for fish species were included in the FishBase information system from its inception. Early tools made use of the relational model and characters like fin ray meristics. Soon pictures and drawings were added as a further help, similar to a field guide. Later came the computerization of existing dichotomous keys, again in combination with pictures and other information, and the ability to restrict possible species by country, area, or taxonomic group. Today, www.FishBase.org offers four different ways to identify species. This paper describes these tools with their advantages and disadvantages, and suggests various options for further development. It explores the possibility of a holistic and integrated computeraided strategy

Modular and cultural factors in biological understanding: an experimental approach to the cognitive basis of science

What follows is a discussion of three sets of experimental results that deal with various aspects of universal biological understanding among American and Maya children and adults. The first set of experiments shows that by the age of four-to-five years (the earliest age tested in this regard) urban American and Yukatek Maya children employ a concept of innate species potential, or underlying essence, as an inferential framework for understanding the affiliation of an organism to a biological species, and for projecting known and unknown biological properties to organisms in the face of uncertainty. The second set of experiments shows that the youngest Maya children do not have an anthropocentric understanding of the biological world. Children do not initially need to reason about non-human living kinds by analogy to human kinds. The third set of results show that the same taxonomic rank is cognitively preferred for biological induction in two diverse populations: people raised in the Mid-western USA and Itza' Maya of the Lowland Meso-american rainforest. This is the generic species the level of oak and robin. These findings cannot be explained by domain-general models of similarity because such models cannot account for why both cultures prefer species-like groups in making inferences about the biological world, although Americans have relatively little actual knowledge or experience at this level. The implication from these experiments is that folk biology may well represent an evolutionary design: universal taxonomic structures, centred on essence-based generic species, are arguably routine products of our ‘habits of mind,' which may be in part naturally selected to grasp relevant and recurrent ‘habits of the world.' The science of biology is built upon these domain-specific cognitive universals: folk biology sets initial cognitive constraints on the development of any possible macro-biological theory, including the initial development of evolutionary theory. Nevertheless, the conditions of relevance under which science operates diverge from those pertinent to folk biology. For natural science, the motivating idea is to understand nature as it is ‘in itself,' independently of the human observer (as far as possible). From this standpoint, the species-concept, like taxonomy and teleology, may arguably be allowed to survive in science as a regulative principle that enables the mind to readily establish stable contact with the surrounding environment, rather than as an epistemic concept that guides the search for truth

BIOMOLECULE INSPIRED DATA SCIENCE

BIOMOLECULE INSPIRED DATA SCIENC

The Question of Method in Theology: An African Response to Bernard Lonergan Using Bantu Theological Anthropology

The question of method in theology has become the locus of contemporary intercultural and cross-cultural theological investigations. For any theological system to claim credulity in the public opinion of theological discourse it must demonstrate credible methodological processes inherent in its epistemological process to affirm the validity of its knowledge claims. It is method in theology which is among the criteria used to evaluate the theological integrity of an epistemic system. This paper, therefore, endeavors to explain the existence of method(s) not only in discursive and formal theologies but also in the theologies of ordinary people and communities alike. The paper demonstrates this affirmation by way of bringing Lonergan’s method in theology into conversation with African Bantu theology by contending that there is an inextricable link between epistemology and theology. Doctrines in theology are first and foremost subjects of revelation which are processed through a particular method. Hence, both Bernard Lonergan’s method and Bantu cultural theological anthropology become legitimate sources of theological knowledge production. Although both epistemic systems affirm the primacy of the consciousness of experience as the first starting point of theology they nevertheless differ in regard to function of theology and the operative process it uses to affirm its statement of faith. Whereas Lonergan’s is individuated and highly speculative Bantu theology is relational, communitarian and overtly functional. Further, Lonergan’s system contends that God can be objectively known by way of authentic subjectivity. Bantu theology, in contrast, posits that God can be known and experienced through participation in the vital force of life. In summary, this thesis contends that in the enterprise of theology there exists a multiplicity of epistemic systems and methodologies which serve specific purposes for a given theological enterprise. It is the foregoing that constitutes the scope, purpose and results of this study

LSST Science Book, Version 2.0

A survey that can cover the sky in optical bands over wide fields to faint magnitudes with a fast cadence will enable many of the exciting science opportunities of the next decade. The Large Synoptic Survey Telescope (LSST) will have an effective aperture of 6.7 meters and an imaging camera with field of view of 9.6 deg^2, and will be devoted to a ten-year imaging survey over 20,000 deg^2 south of +15 deg. Each pointing will be imaged 2000 times with fifteen second exposures in six broad bands from 0.35 to 1.1 microns, to a total point-source depth of r~27.5. The LSST Science Book describes the basic parameters of the LSST hardware, software, and observing plans. The book discusses educational and outreach opportunities, then goes on to describe a broad range of science that LSST will revolutionize: mapping the inner and outer Solar System, stellar populations in the Milky Way and nearby galaxies, the structure of the Milky Way disk and halo and other objects in the Local Volume, transient and variable objects both at low and high redshift, and the properties of normal and active galaxies at low and high redshift. It then turns to far-field cosmological topics, exploring properties of supernovae to z~1, strong and weak lensing, the large-scale distribution of galaxies and baryon oscillations, and how these different probes may be combined to constrain cosmological models and the physics of dark energy.Comment: 596 pages. Also available at full resolution at http://www.lsst.org/lsst/sciboo

Decay fungi associated with cavity excavation by a large South American woodpecker

In temperate systems of the Northern Hemisphere, wood-decay fungi are known to facilitate cavity excavation by woodpeckers. For South America, woodpecker–fungi interactions have not been explored. The aim of this work was to identify wooddecay fungi associated with the process of cavity excavation by the Magellanic woodpecker (Campephilus magellanicus), a large South American picid that excavates on living trees. The survey was conducted in old-growth Nothofagus pumilio forests of Patagonia. For freshly excavated cavities, wood condition was assessed, adjacent basidiocarps were collected, and fungal cultures were obtained from wood samples taken to the laboratory. All cavities exhibited softened wood. Four Agaricomycotina were isolated in cultures: Stereum hirsutum was the most frequent, followed by Postia pelliculosa, Nothophellinus andinopatagonicus and Aurantiporus albidus. Basidiocarps around cavities were of two species that did not develop in cultures: Laetiporus portentosus and Macrohyporia dictyopora. Excavations were slightly more frequent in white rot colonized than brown rot colonized wood, but this may be an artefact of differential success in fungal isolation and culturing, since several cavities that showed visual symptoms of brown wood rots did not yield mycelia of those wooddecay fungi. As shown by research elsewhere, basidiocarps underestimated heart rot on cavity walls and revealed additional wood-decay species living on the same trees; therefore, assessments of fungal diversity in substrates used for cavity excavation should be based on culturing and/or DNA extraction. Because fungal communities in the southern Andes are poorly known, decay fungi and their roles in ecosystem development should be studied across different forest areas, where samples from non-cavity-bearing (control) trees should also be taken in order to determine excavation-site selection.Fil: Pozzi, Carla Martina. Ministerio de Ambiente y Desarrollo Sustentable. Administración de Parques Nacionales. Parque Nacional "Nahuel Huapi". Departamento Conservación y Educación Ambiental; ArgentinaFil: Rajchenberg, Mario. Centro de Investigación y Extensión Forestal Andino Patagónico; Argentina. Universidad Nacional de la Patagonia "San Juan Bosco"; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico; ArgentinaFil: Ojeda, Valeria Susana. Consejo Nacional de Investigaciones Cientificas y Tecnicas. Centro Cientifico Tecnologico Conicet - Patagonia Norte. Instituto de Investigaciones En Biodiversidad y Medioambiente. Subsede Junín de Los Andes-inibioma-centro de Ecología Aplicada del Neuquén (cean) | Universidad Nacional del Comahue. Centro Regional Universitario Bariloche. Instituto de Investigaciones En Biodiversidad y Medioambiente. Subsede Junín de Los Andes-inibioma-centro de Ecología Aplicada del Neuquén (cean).; Argentin

Visualização de padrões temporais cíclicos em estudos de fenologia

Orientadores: Ricardo da Silva Torres, Leonor Patrícia Cerdeira MorellatoTese (doutorado) - Universidade Estadual de Campinas, Instituto de ComputaçãoResumo: Em diversas aplicações, grandes volumes de dados multidimensionais têm sido gerados continuamente ao longo do tempo. Uma abordagem adequada para lidar com estas coleções consiste no uso de métodos de visualização de informação, a partir dos quais padrões de interesse podem ser identificados, possibilitando o entendimento de fenômenos temporais complexos. De fato, em diversos domínios, o desenvolvimento de ferramentas adequadas para apoiar análises complexas, por exemplo, aquelas baseadas na identificação de padrões de mudanças ou correlações existentes entre múltiplas variáveis ao longo do tempo é de suma importância. Em estudos de fenologia, por exemplo, especialistas observam as mudanças que ocorrem ao longo da vida de plantas e animais e investigam qual é a relação entre essas mudanças com variáveis ambientais. Neste cenário, especialistas em fenologia cada vez mais precisam de ferramentas para, adequadamente, visualizar séries temporais longas, com muitas variáveis e de diferentes tipos (por exemplo, texto e imagem), assim como identificar padrões temporais cíclicos. Embora diversas abordagens tenham sido propostas para visualizar dados que variam ao longo do tempo, muitas não são apropriadas ou aplicáveis para dados de fenologia, porque não são capazes de: (i) lidar com séries temporais longas, com muitas variáveis de diferentes tipos de dados e de uma ou mais dimensões; e (ii) permitir a identificação de padrões temporais cíclicos e drivers ambientais associados. Este trabalho aborda essas questões a partir da proposta de duas novas abordagens para apoiar a análise e visualização de dados temporais multidimensionais. Nossa primeira proposta combina estruturas visuais radiais com ritmos visuais. As estruturas radiais são usadas para fornecer informação contextual sobre fenômenos cíclicos, enquanto que o ritmo visual é usado para sumarizar séries temporais longas em representações compactas. Nós desenvolvemos, avaliamos e validamos nossa proposta com especialistas em fenologia em tarefas relacionadas à visualização de dados de observação direta da fenologia de plantas em nível tanto de indivíduos quanto de espécies. Nós também validamos a proposta usando dados temporais relacionados a imagens obtidas de sistemas de monitoramento de vegetação próxima à superfície. Nossa segunda abordagem é uma nova representação baseada em imagem, chamada Change Frequency Heatmap (CFH), usada para codificar mudanças temporais de dados numéricos multivariados. O método calcula histogramas de padrões de mudanças observados em sucessivos instantes de tempo. Nós validamos o uso do CFH a partir da criação de uma ferramenta de caracterização de mudanças no ciclo de vida de plantas de múltiplos indivíduos e espécies ao longo do tempo. Nós demonstramos o potencial do CFH para ajudar na identificação visual de padrões de mudanças temporais complexas, especialmente na identificação de variações entre indivíduos em estudos relacionados à fenologia de plantasAbstract: In several applications, large volumes of multidimensional data have been generated continuously over time. One suitable approach for handling those collections in a meaningful way consists in the use of information visualization methods, based on which patterns of interest can be identified, triggering the understanding of complex temporal phenomena. In fact, in several domains, the development of appropriate tools for supporting complex analysis based, for example, on the identification of change patterns in temporal data or existing correlations, over time, among multiple variables, is of paramount importance. In phenology studies, for instance, phenologists observe changes in the development of plants and animals throughout their lives and investigate what is the relationship between these changes with environmental changes. Therefore, phenologists increasingly need tools for visualizing appropriately long-term series with many variables of different data types, as well as for identifying cyclical temporal patterns. Although several approaches have been proposed to visualize data varying over time, most of them are not appropriate or applicable to phenology data, because they are not able: (i) to handle long-term series with many variables of different data types and one or more dimensions and (ii) to support the identification of cyclical temporal patterns and associated environmental drivers. This work addresses these shortcomings by presenting two new approaches to support the analysis and visualization of multidimensional temporal data. Our first proposal to visualize phenological data combines radial visual structures along with visual rhythms. Radial visual structures are used to provide contextual insights regarding cyclical phenomena, while the visual rhythm encoding is used to summarize long-term time series into compact representations. We developed, evaluated, and validated our proposal with phenology experts using plant phenology direct observational data both at individuals and species levels. Also we validated the proposal using image-related temporal data obtained from near-surface vegetation monitoring systems. Our second approach is a novel image-based representation, named Change Frequency Heatmap (CFH), used to encode temporal changes of multivariate numerical data. The method computes histograms of change patterns observed at successive timestamps. We validated the use of CFHs through the creation of a temporal change characterization tool to support complex plant phenology analysis, concerning the characterization of plant life cycle changes of multiple individuals and species over time. We demonstrated the potential of CFH to support visual identification of complex temporal change patterns, especially to decipher interindividual variations in plant phenologyDoutoradoCiência da ComputaçãoDoutora em Ciência da Computação162312/2015-62013/501550-0CNPQCAPESFAPES